package org.tcdb.biotools;

import org.biojava3.core.sequence.ProteinSequence;

public interface IExtendedAlignment {

	public void setShuffles();
	public int getShuffles();
	
	public void setSubject(String fasta);
	public void setSubject(ProteinSequence subject);
	public ProteinSequence getSubject();
	
	public void setTarget(String fasta);
	public void setTarget(ProteinSequence target);
	public ProteinSequence getTarget();
	
	public String toString();
	
	public void setAlignment();
	
	public void executeComparison();
}
